Chemical Science Blog

A small consolation when marking undergraduate organic chemistry exams is that occasionally you come across an answer so ridiculous it is almost brilliant. Penned to complete a far-fetched synthesis, the student managed to propose a reaction that is completely without precedent, not only in the course, but in the chemistry literature as a whole. Sadly for the student it is completely wrong, 0 marks.

I imagine that 50 years ago if an undergraduate student had proposed a one-step synthesis of γ-lactams starting with a linear alkylamine, which proceeded by clipping off an N-H bond and a C-H bond, then stitching it together with a carbon monoxide molecule at the junction, they too may have got 0 marks. Yet Matthew Gaunt and researchers in his laboratory at the University of Cambridge have achieved just this via palladium-catalysed C-H activation.

Transition metal-catalysed C-H activation refers to the cleavage of a C-H bond by a transition metal, followed by functionalisation of the metal-bound organic fragment and regeneration of the catalyst. This strategy is counter to the classical approach of organic synthesis: construction of molecular complexity by installing and manipulating reactive functional groups. The object of pre-functionalisation is two-fold: it makes a molecule more reactive (for example, installation of a halide can enable oxidative addition to a transition metal or substitution by a nucleophile) and it directs reactivity to a specific location in the molecule under construction. For C-H activation the challenge is to promote reaction of thermodynamically and kinetically stable C-H bonds, and achieve site-selectivity in a molecule containing many chemically-similar C-H bonds.

Figure 1: Optimised reaction conditions

The authors found that a catalytic system consisting of palladium pivalate and copper acetate, in combination with acidic and basic additives under a CO/air atmosphere, transformed a variety of secondary amines with primary C-H bonds at the γ-position into 5-membered lactones (Figure 1). Good yields and diastereoselectivities were obtained, and a variety of substituents such as carbocycles, tetrahydropyran, piperadine, fluorocycloalkanes and dioxolanes were well tolerated.

Figure 2: Mechanistic hypothesis showing organisation of the transition state and C-H activation.

The reacting components in the C-H activation step are highly organised in the transition state by coordination of the amine to the palladium centre, and formation of a hydrogen bond between the amine and the carbonyl group of a pivalate ligand bound to palladium (Figure 2). Palladium insertion into the C-H bond (one of the pivalate ligands serves as an intramolecular base) forms a palladacycle with the entropic and enthalpic preference for a 5-membered ring, necessitating abstraction of a proton in the γ-position with respect to the amine directing group.

C-H activation has been referred to as the ‘holy grail’ of catalysis, and the efficiency gains are clear: reduction in reaction steps and use of catalysis minimises energy use, formation of stoichiometric by-products and waste from isolation and purification processes, excess reagents, solvents and additives. This aside, the most exciting thing about the development of C-H activation methods is the promise of discovery: novel reactivity can lead to novel products, inaccessible by other means.

To find out more please read:

Diastereoselective C-H carbonylative annulation of aliphatic amines: a rapid route to functionalized γ-lactams

Png Zhuang Mao, Jaime R. Cabrera-Pardo, Jorge Piero Cadahia and Matthew J. Gaunt.
Chem. Sci., 2018, Edge Article
DOI: 10.1039/c8sc02855a

About the author

Zoë Hearne is a PhD candidate in chemistry at McGill University in Montréal, Canada, under the supervision of Professor Chao-Jun Li. She hails from Canberra, Australia, where she completed her undergraduate degree. Her current research focuses on transition metal catalysis to effect novel transformations, and out of the lab she is an enthusiastic chemistry tutor and science communicator.

We happily breathe our dinitrogen-rich atmosphere all day, but to access nitrogen for the biosynthesis of molecules such as DNA, RNA and proteins, we rely on nitrogen fixation to reduce dinitrogen into bioavailable molecules like ammonia. In nature, nitrogen-fixing bacteria and archaea equipped with nitrogenase enzymes are responsible for providing plants with reduced nitrogen, which makes its way back to us. Nitrogenase is an enzyme complex of two proteins. The first consists of an iron-containing reductase that supplies electrons to the iron/molybdenum-containing catalytic protein, which carries out the N₂ to NH₃ conversion.

The Haber Bosch process, an industrial method for fixing dinitrogen into ammonia, was first applied in the early 1900’s and generated a huge supply of nitrogen-based fertilizers to synthetically provide plants with this essential nutrient. The population boom that resulted, and with it the global importance of this reaction, has yet to abate. Albeit an efficient reaction, this iron-catalysed process requires high temperatures (450 °C) and pressures (200 atm). In comparison, enzymes can operate under conditions synthetic chemists can only dream of, as researchers at the University of Utah have demonstrated in their work on the bioelectrochemical reduction of dinitrogen under ambient conditions using the catalytic nitrogenase protein.

The researchers synthesised an electrode/enzyme aggregate by trapping the nitrogenase enzyme in a hydrogel, then binding the hydrogel via π-stacking of incorporated pyrene motifs to carbon paper electrodes coated in multi-walled carbon nanotubes. If the enzyme is oriented in the hydrogel in such a way that the distance between the catalytic iron/molybdenum centre of the enzyme and the electrode is within 14 Å, direct electron transfer can take place. Direct electrical contact with enzymes allows researchers to take advantage of the high efficiency and selectivity of enzymes for conducting chemical reactions under mild conditions.

Two methods for immobilization of proteins on an electrode: the docking strategy (upper) and the hydrogel strategy (middle). Active protein is green, while inactive/denatured protein is grey. π-stacking of pyrene moieties within the polymer binds the hydrogel to the carbon nanotubes (lower).

To minimise the distance between the enzyme’s redox centre and the electrode, prior strategies have focused on docking enzymes in the desired configuration; however low enzyme activities can result due to protein denaturation. The authors of this work designed a system under the hypothesis that if they focussed on preserving enzymatic activity, the statistical mixture of configurations adopted by enzymes in the hydrogel would still contain a large proportion capable of participating in direct electron transfer.

Bioelectrical activity of the electrode/nitrogenase aggregate was assessed under bubbling N₂ at room temperature, and 180 nmol of NH₃ (1.1 μmol/mg nitrogenase enzyme) was produced, marking the first bioelectrochemical reduction of N₂ in the absence of ATP. The bioelectrical activity of laccase for the reduction of O₂ was also measured using the same method. In this experiment 15% of laccase proteins remained active, compared to 0.3% using a reference method applying an enzyme docking technique. This translated to increased current densities of 390 – 1880 μA cm^-2 mg^-1 (depending on the enzyme concentration, 1-10 mg mL^-1) compared to 45 μA cm^-1 mg^-1 for the reference docking method.

Without being too grandiose, synthetic nitrogen fixation is vital for the continued survival of people on the planet (how did I do?). Beyond nitrogen fixation, this research offers a general method to achieve contact between a conductive electrode and the highly complex catalytic machinery that nature offers: enzymes. Beyond synthesis, opportunities broaden; technology such as this might pave the way for the production of biosensors, biofuel cells and biomolecular electronic components.

To find out more please read:

Pyrene hydrogel for promoting direct bioelectrochemistry: ATP-independent electroenzymatic reduction of N₂

David P. Hickey, Koun Lim, Rong, Cai, Ashlea R. Patterson, Mengwei Yuan, Selmihan Sahin, Sofiene Abdellaoui, Shelley D. Minteer
Chem. Sci., 2018, 9, 5172-5177
DOI: 10.1039/c8sc01638k

About the author:

Zoë Hearne is a PhD candidate in chemistry at McGill University in Montréal, Canada, under the supervision of Professor Chao-Jun Li. She hails from Canberra, Australia, where she completed her undergraduate degree. Her current research focuses on transition metal catalysis to effect novel transformations, and out of the lab she is an enthusiastic chemistry tutor and science communicator.

Proteins have an expansive utility in the structure, function, replication and regulation of all cells, and developing tools to study each role is to the benefit of our continued health and wellbeing. One tool is protein bioconjugation, the covalent pairing of a molecule with a protein. Molecule-protein combinations are endless, provided there are efficient methods available to couple molecules with amino acids. Among bioconjugation methods, cysteine functionalisation is a popular choice because the primary thiol is highly nucleophilic thus aiding chemoselectivity. Furthermore, cysteine is rare, reducing the likelihood of many competing, reactive residues.

Transition metal catalysed transformations are uncommon in bioconjugations, despite prominence in other areas of synthetic chemistry. This is because only the most robust methods can overcome the challenges of this chemistry: the solubility of substrates in solvents other than aqueous media, the presence of other amino acids bearing reactive functional groups, and the requirement for low temperatures, low concentrations and mild pH to preserve protein structure.

Catalytic cycle for the nickel/phororedox catalysed synthesis of cysteine bioconjugates

A group of researchers from the University of Pennsylvania headed by Professor Gary Molander have developed a bioconjugation method in which aryl halides are cross-coupled with cysteine residues in peptides. Two complexes catalyse the reaction in two connected cycles: the photoredox cycle by a ruthenium-bipyridine complex_, and the catalytic cycle by a nickel-bipyridine complex.

The reaction is efficient at room temperature and does not require prior functional group protection. The reaction can also be performed under dilute conditions (10 mM) and on gram scale (3.5 mmol). The scope table includes more than 35 reactions coupling a broad range of aryl halides with small peptides (4 and 9 amino acids) and biologically relevant molecules such as coenzyme A and sulphur-containing pharmaceuticals.

Protecting group free functionalisation of small peptides under dilute conditions

Included in the reaction scope are a number of substrates which highlight how this work can adapt to established techniques for studying proteins. Coupling of a coumarin generates a fluorescent molecule, which could be used to study the cellular localisation of a protein. Reaction with an aryl-bound biotin derivative demonstrates that affinity tags can be coupled, and utilising aryl-containing pharmaceutical agents is relevant to the synthesis of antibody-drug conjugates.

With this research the authors have contributed a robust catalytic system, which convincingly shows the value of combining a transition metal and photoredox catalyst to functionalise cysteine residues in biomolecules. A necessary next step for this chemistry, and no small task, is to further optimise the reaction conditions for whole proteins.

Read the research article:

Scalable thioarylation of unprotected peptides and biomolecules under Ni/photoredox catalysis

Chem. Sci., 2018, DOI: 10.1039/C7SC04292B

Brandon A. Vara, Xingpin Li, Simon Berritt, Christopher R. Walters, E. James Petersson, Gary A. Molander.

About the Author: 

Zoë Hearne is a PhD candidate in chemistry at McGill University in Montréal, Canada, under the supervision of Professor Chao-Jun Li. She hails from Canberra, Australia, where she completed her undergraduate degree. Her current research focuses on transition metal catalysis to effect novel transformations, and out of the lab she is an enthusiastic chemistry tutor and science communicator.

For the first time, a group of scientists from University of California, San Diego in United States has quantitatively measured the strength of hydrogen bonds between two complex molecules. They also observed an abnormal trend regarding the bond strength in the absence and presence of electron transfer. This work contributes to the understanding of how the hydrogen bond strength changes, an important point that reveals the way biological systems function.

Hydrogen bonds are a type of electrostatic attraction between hydrogen atoms and certain highly electronegative atoms including N, O and F. These bonds help to bind individual water molecules together and keep water as liquid at room temperature, a critical condition for the origin of life.

The researchers, led by Prof. Kubiak, picked two ruthenium-based complexes joined by hydrogen bonds as their studying platform. As shown in Figure 1, the two-molecule system has three states depending on whether the ends are charged or not: the neutral state when both ends are not charged (left), the singly reduced state when only one end is negatively charged (middle), and the doubly reduced state when both ends are negatively charged (right). The group utilized infrared spectroscopy, UV-vis spectroscopy and electrochemical measurements to experimentally determine the strength of hydrogen bonds in these different redox states.

The results from the study found that the hydrogen bond energy of the neutral state and the doubly reduced state was in the range of 2.56-2.88 kcal/mol and 4.50-4.63 kcal/mol, respectively. Surprisingly, the hydrogen bond energy of the singly charged state did not lie between that of the neutral state and the doubly reduced state. It ranged from 7.78 kcal/mol to 8.31 kcal/mol, indicating the hydrogen bond is much stronger than for both the neutral and doubly-reduced states. The authors ascribed such an abnormality to the reinforcement brought by electron transfer i.e., the movement of the negative charge between the two ends.

This work is the first demonstration that hydrogen bond strength can be significantly enhanced by electron delocalization.

Figure 1. A schematic diagram showing the hydrogen bond strength of the singly reduced state (middle), the neutral state (left) and the doubly reduced states (right). [Note: In this figure, the lower the state lies, the stronger its hydrogen bond is. ET: electron transfer.]

Effects of Electron Transfer on the Stability of Hydrogen Bonds

Tyler M. Porter, Gavin P. Heim and Clifford P. Kubiak

Chem. Sci. DOI: 10.1039/c7sc03361c

About the blogger:

Tianyu Liu is a Ph.D. in chemistry graduated from University of California, Santa Cruz in United States. He is passionate about scientific communication to introduce cutting-edge researches to both the general public and the scientists with diverse research expertise. He is a web blogger for the Chem. Commun. and Chem. Sci. blog websites. More information about him can be found at http://liutianyuresearch.weebly.com/.